5MTF

A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.

Ticha, A.Stanchev, S.Vinothkumar, K.R.Mikles, D.C.Pachl, P.Began, J.Skerle, J.Svehlova, K.Nguyen, M.T.N.Verhelst, S.H.L.Johnson, D.C.Bachovchin, D.A.Lepsik, M.Majer, P.Strisovsky, K.

(2017) Cell Chem Biol 24: 1523-1536.e4

  • DOI: https://doi.org/10.1016/j.chembiol.2017.09.007
  • Primary Citation of Related Structures:  
    5MT6, 5MT7, 5MT8, 5MTF

  • PubMed Abstract: 

    Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery.


  • Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic; First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhomboid protease GlpG190Escherichia coli S88Mutation(s): 0 
Gene Names: glpGECS88_3813
EC: 3.4.21.105
Membrane Entity: Yes 
UniProt
Find proteins for P09391 (Escherichia coli (strain K12))
Explore P09391 
Go to UniProtKB:  P09391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09391
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
inhibitorB [auth C]6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.365α = 90
b = 111.365β = 90
c = 124.539γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary